There should be an ocn.dat file that corresponds to the CSD base name that you passed to mri_glmfit-sim. The cache just uses a pre-computed table. The computations are pretty simple. It synthesizes white gaussian noise on the surface, smooths it by a certain amount, then finds clusters at various thresholds and signs. It tabulates how likely a cluster of a given size is given the smoothing level, threshold, and sign. doug
On 04/16/2012 09:10 PM, zhang mingxia wrote: > Hi Doug, > > Thanks. I have done Clusterwise Correction for Multiple Comparisons, > so there is some file like mc-z.positive.y.ocn.dat. I have seen the > column. > > By the way, I just know the clusterwise correction(which I get > the mc-z. files) use the permutation method. What about the "--cache" > one? Is there any introduction on website? I have not seen any. > > Thanks again. > > Mingxia > > On Thu, Apr 12, 2012 at 10:33 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Hi Zhang, there should be a file named something like > "cache.th13.abs.y.ocn.dat" that is output as part of the > correction for > multiple comparisons. This will have a column for each significant > cluster in the order that the clusters are in. Each row is a > subject. So > you can take the mean over the subjects to get the number you want. > doug > > > On 04/10/2012 08:01 PM, zhang mingxia wrote: > > Dear Freesurfer experts, > > > > I have done the whole brain analysis and get some significant > > clusters. How can I get the mean thickness of these clusters of > every > > subject? > > > > Thank you very much. > > > > Mingxia Zhang > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
